Variant report

Variant	rs12642246
Chromosome Location	chr4:166285761-166285762
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11944875	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12498302	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12501589	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12502374	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12503472	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12509710	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12513198	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13113058	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13123297	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13151882	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1347744	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1370683	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1438112	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17624714	0.89[ASN][1000 genomes]
rs17686668	0.89[ASN][1000 genomes]
rs35411578	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4621390	0.87[ASN][1000 genomes]
rs4690812	0.87[ASN][1000 genomes]
rs875486	0.90[EUR][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12642246	SNORD96A	trans	cerebellum	SCAN
rs12642246	CPE	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:166281600-166285800	Weak transcription	Hela-S3	cervix
2	chr4:166282600-166290800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr4:166282800-166286000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr4:166283600-166288600	Enhancers	Fetal Intestine Large	intestine
5	chr4:166284400-166287600	Enhancers	Fetal Intestine Small	intestine
6	chr4:166284800-166286000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr4:166284800-166286000	Enhancers	Pancreatic Islets	Pancreatic Islet
8	chr4:166284800-166286800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr4:166285000-166286000	Enhancers	Rectal Mucosa Donor 31	rectum
10	chr4:166285400-166286800	Enhancers	HMEC	breast
11	chr4:166285400-166290000	Enhancers	HepG2	liver
12	chr4:166285600-166285800	Enhancers	Rectal Mucosa Donor 29	rectum
13	chr4:166285600-166286400	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr4:166285600-166286600	Enhancers	HUES48 Cell Line	embryonic stem cell

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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